Ok... got it done... but surprising, it was NOT anything like the SIB 51 07 04 described.

The dealer actually replaced the "Inner Windows Trims" on all four doors. They are the black plastic trim surrounding the inner side of window frames. NOT THE DOOR SEAL

Drove it for about 30 min from the workshop back home with Radio switched off. The squeaky noise seems to have gone away completely.... Phew...

Take your X3 to the dealer now if you are experiencing any squeaky noise!!!

(Edited: the noise came back, please continue to read below)